Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

John P Hammond^*³ , Martin R Broadley^*² , David J Craigon¹ , Janet Higgins¹ , Zoe F Emmerson¹ , Henrik J Townsend¹ , Philip J White³ and Sean T May¹

¹Nottingham Arabidopsis Stock Centre, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK

²Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK

³Warwick HRI, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK

author email corresponding author email* Contributed equally

Plant Methods 2005, 1:10doi:10.1186/1746-4811-1-10


Published:	9 November 2005

Additional files

Additional File 1:

An archive of the mean probe-set signals of all genes in P-starved versus control (P-replete) Brassica oleracea var. alboglabra cv. A12DHd. Raw data were analysed with the RMA pre-normalisation algorithm using the ATH1-121501 probe mask file (no probe selection) or a custom probe mask file. The custom probe mask files were generated by hybridising gDNA from B. oleracea to Affymetrix A. thaliana ATH-121501 GeneChip^®arrays and selecting probe-pairs in which B. oleracea gDNA hybridisation intensity values were greater than 50, 100, 150, 200, 300,...1000. Signal intensities are estimates from total RNA extracted from the shoots of hydroponically-grown plants (n = 4) under P-deficient (raw) and P-replete (control) conditions. The P-values are derived from a one-way ANOVA using a Benjamini and Hochberg False Discovery Rate (0.05) multiple testing correction.

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Additional File 2:

An archive containing all of the Perl scripts necessary in order to produce new CDF files for use in analysing cross-species hybridisation results.

Format: ZIP Size: 25KB Download file

Additional File 3:

(CDF_filtering script instructions.doc : DOC file). An instruction document containing details for using the scripts contained within 2.

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